# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 14:16:23 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CN[C@H]2CCCN[C@H]2c3ccccc3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 GBK  GBK  (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine  ligand  46  22  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GBK
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 GBK  C10  C  CH2   0  -0.448   0.6356   2.5794  -1.2580
 GBK  C13  C  CH1   0  -0.120   2.2747   1.1514  -0.0388
 GBK  C17  C  CR6   0   0.087   2.7971  -0.2440   0.2054
 GBK  C20  C  CR16  0  -0.269   3.7344  -2.8618   0.5486
 GBK  C21  C  CR16  0  -0.243   4.1022  -2.1280  -0.5732
 GBK  C22  C  CR16  0  -0.303   3.6381  -0.8317  -0.7389
 GBK  C01  C  CH3   0  -0.435  -3.8813   1.9207   0.8459
 GBK  C02  C  CR6   0   0.361  -3.0797  -0.1348  -0.0331
 GBK  C03  C  CR16  0  -0.385  -4.0946  -0.8608   0.5849
 GBK  C04  C  CR16  0  -0.254  -4.1668  -2.2402   0.4163
 GBK  C05  C  CR16  0  -0.273  -3.2381  -2.9030  -0.3662
 GBK  C06  C  CR16  0  -0.294  -2.2280  -2.1683  -0.9797
 GBK  C07  C  CR6   0  -0.006  -2.1288  -0.7932  -0.8319
 GBK  C08  C  CH2   0  -0.323  -1.0024  -0.0361  -1.4786
 GBK  C09  C  CH1   0  -0.053   1.0807   1.1364  -1.0163
 GBK  C11  C  CH2   0  -0.427   0.3155   3.2727   0.0587
 GBK  C12  C  CH2   0  -0.291   1.5082   3.1911   0.9972
 GBK  N14  N  NH1   0  -0.586  -0.0118   0.3415  -0.4870
 GBK  N15  N  NH1   0  -0.597   1.9016   1.8059   1.1999
 GBK  C18  C  CR16  0  -0.315   2.4360  -0.9873   1.3271
 GBK  C19  C  CR16  0  -0.240   2.9020  -2.2861   1.4975
 GBK  H1   H  HCH2  0   0.217   1.4447   3.1089  -1.7720
 GBK  H2   H  HCH2  0   0.235  -0.2240   2.6141  -1.9301
 GBK  H3   H  HCH1  0   0.214   3.0702   1.7080  -0.5671
 GBK  H4   H  HCR6  0   0.254   4.0975  -3.8725   0.6829
 GBK  H5   H  HCR6  0   0.254   4.7558  -2.5651  -1.3172
 GBK  H6   H  HCR6  0   0.245   3.9391  -0.2652  -1.6134
 GBK  H7   H  HCH3  0   0.227  -4.8973   1.8351   0.4500
 GBK  H8   H  HCH3  0   0.226  -3.8843   1.5987   1.8906
 GBK  H9   H  HCH3  0   0.256  -3.5770   2.9638   0.8035
 GBK  H10  H  HCR6  0   0.276  -4.8382  -0.3707   1.1990
 GBK  H11  H  HCR6  0   0.255  -4.9624  -2.7888   0.9039
 GBK  H12  H  HCR6  0   0.248  -3.2935  -3.9750  -0.5013
 GBK  H13  H  HCR6  0   0.248  -1.4936  -2.6773  -1.5935
 GBK  H14  H  HCH2  0   0.208  -0.5788  -0.6536  -2.2866
 GBK  H15  H  HCH2  0   0.235  -1.3897   0.8642  -1.9591
 GBK  H16  H  HCH1  0   0.209   1.4602   0.7255  -1.9683
 GBK  H17  H  HCH2  0   0.222   0.0570   4.3200  -0.1123
 GBK  H18  H  HCH2  0   0.231  -0.5510   2.7919   0.5158
 GBK  H19  H  HCH2  0   0.183   2.3294   3.7965   0.5768
 GBK  H20  H  HCH2  0   0.230   1.2612   3.6260   1.9681
 GBK  H21  H  HNH1  0   0.344   0.3550  -0.5091  -0.0767
 GBK  H23  H  HNH1  0   0.349   2.6886   1.7752   1.8361
 GBK  H25  H  HCR6  0   0.254   1.7876  -0.5467   2.0735
 GBK  H26  H  HCR6  0   0.253   2.6107  -2.8481   2.3759
 GBK  O16  O  O2    0  -0.456  -2.9470   1.2000   0.0716

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 GBK  C12  C11  single    1.520  0.020  1.520
 GBK  C12  N15  single    1.454  0.020  1.454
 GBK  C11  C10  single    1.522  0.020  1.522
 GBK  N15  C13  single    1.450  0.020  1.450
 GBK  C10  C09  single    1.529  0.020  1.529
 GBK  C13  C09  single    1.543  0.020  1.543
 GBK  C13  C17  single    1.510  0.020  1.510
 GBK  C09  N14  single    1.451  0.020  1.451
 GBK  C17  C22  aromatic  1.394  0.020  1.394
 GBK  C17  C18  aromatic  1.393  0.020  1.393
 GBK  N14  C08  single    1.452  0.020  1.452
 GBK  C22  C21  aromatic  1.387  0.020  1.387
 GBK  C18  C19  aromatic  1.390  0.020  1.390
 GBK  C08  C07  single    1.503  0.020  1.503
 GBK  C21  C20  aromatic  1.390  0.020  1.390
 GBK  C19  C20  aromatic  1.387  0.020  1.387
 GBK  C07  C06  aromatic  1.387  0.020  1.387
 GBK  C07  C02  aromatic  1.406  0.020  1.406
 GBK  O16  C02  single    1.346  0.020  1.346
 GBK  O16  C01  single    1.411  0.020  1.411
 GBK  C06  C05  aromatic  1.392  0.020  1.392
 GBK  C02  C03  aromatic  1.393  0.020  1.393
 GBK  C05  C04  aromatic  1.383  0.020  1.383
 GBK  C03  C04  aromatic  1.392  0.020  1.392
 GBK  C10  H1   single    0.970  0.020  1.090
 GBK  C10  H2   single    0.970  0.020  1.090
 GBK  C13  H3   single    0.970  0.020  1.090
 GBK  C20  H4   single    0.930  0.020  1.080
 GBK  C21  H5   single    0.930  0.020  1.080
 GBK  C22  H6   single    0.930  0.020  1.080
 GBK  C01  H7   single    0.970  0.020  1.090
 GBK  C01  H8   single    0.970  0.020  1.090
 GBK  C01  H9   single    0.970  0.020  1.090
 GBK  C03  H10  single    0.930  0.020  1.080
 GBK  C04  H11  single    0.930  0.020  1.080
 GBK  C05  H12  single    0.930  0.020  1.080
 GBK  C06  H13  single    0.930  0.020  1.080
 GBK  C08  H14  single    0.970  0.020  1.090
 GBK  C08  H15  single    0.970  0.020  1.090
 GBK  C09  H16  single    0.970  0.020  1.090
 GBK  C11  H17  single    0.970  0.020  1.090
 GBK  C11  H18  single    0.970  0.020  1.090
 GBK  C12  H19  single    0.970  0.020  1.090
 GBK  C12  H20  single    0.970  0.020  1.090
 GBK  N14  H21  single    0.890  0.020  1.040
 GBK  N15  H23  single    0.890  0.020  1.040
 GBK  C18  H25  single    0.930  0.020  1.080
 GBK  C19  H26  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 GBK  H2   C10  H1   106.11  3.000
 GBK  H2   C10  C11  110.64  3.000
 GBK  H1   C10  C11  109.95  3.000
 GBK  H2   C10  C09  110.88  3.000
 GBK  H1   C10  C09  108.38  3.000
 GBK  C11  C10  C09  110.75  3.000
 GBK  H3   C13  N15  111.48  3.000
 GBK  H3   C13  C09  105.01  3.000
 GBK  N15  C13  C09  110.27  3.000
 GBK  H3   C13  C17  107.08  3.000
 GBK  C09  C13  C17  111.17  3.000
 GBK  N15  C13  C17  111.59  3.000
 GBK  C18  C17  C22  118.47  3.000
 GBK  C18  C17  C13  122.25  3.000
 GBK  C22  C17  C13  119.25  3.000
 GBK  H4   C20  C19  120.27  3.000
 GBK  H4   C20  C21  120.29  3.000
 GBK  C19  C20  C21  119.45  3.000
 GBK  H5   C21  C22  119.83  3.000
 GBK  H5   C21  C20  120.08  3.000
 GBK  C22  C21  C20  120.09  3.000
 GBK  H6   C22  C21  119.46  3.000
 GBK  H6   C22  C17  119.55  3.000
 GBK  C21  C22  C17  120.99  3.000
 GBK  H9   C01  H8   108.70  3.000
 GBK  H9   C01  H7   108.73  3.000
 GBK  H8   C01  H7   108.68  3.000
 GBK  H9   C01  O16  106.45  3.000
 GBK  H8   C01  O16  112.06  3.000
 GBK  H7   C01  O16  112.11  3.000
 GBK  O16  C02  C07  116.25  3.000
 GBK  O16  C02  C03  123.68  3.000
 GBK  C07  C02  C03  120.07  3.000
 GBK  H10  C03  C04  118.83  3.000
 GBK  H10  C03  C02  121.11  3.000
 GBK  C04  C03  C02  120.06  3.000
 GBK  H11  C04  C05  120.36  3.000
 GBK  H11  C04  C03  119.07  3.000
 GBK  C05  C04  C03  120.57  3.000
 GBK  H12  C05  C06  120.35  3.000
 GBK  H12  C05  C04  120.72  3.000
 GBK  C06  C05  C04  118.93  3.000
 GBK  H13  C06  C07  118.53  3.000
 GBK  H13  C06  C05  119.57  3.000
 GBK  C07  C06  C05  121.90  3.000
 GBK  C08  C07  C06  120.47  3.000
 GBK  C06  C07  C02  118.47  3.000
 GBK  C08  C07  C02  121.03  3.000
 GBK  H15  C08  H14  106.02  3.000
 GBK  H15  C08  N14  109.16  3.000
 GBK  H14  C08  N14  112.61  3.000
 GBK  H15  C08  C07  109.81  3.000
 GBK  H14  C08  C07  108.75  3.000
 GBK  N14  C08  C07  110.39  3.000
 GBK  H16  C09  N14  111.68  3.000
 GBK  H16  C09  C13  106.48  3.000
 GBK  N14  C09  C13  110.91  3.000
 GBK  H16  C09  C10  108.35  3.000
 GBK  N14  C09  C10  110.82  3.000
 GBK  C13  C09  C10  108.43  3.000
 GBK  H18  C11  H17  107.47  3.000
 GBK  H18  C11  C12  109.93  3.000
 GBK  H17  C11  C12  109.50  3.000
 GBK  H18  C11  C10  109.19  3.000
 GBK  H17  C11  C10  110.55  3.000
 GBK  C12  C11  C10  110.16  3.000
 GBK  H20  C12  H19  106.76  3.000
 GBK  H20  C12  N15  108.45  3.000
 GBK  H19  C12  N15  111.99  3.000
 GBK  H20  C12  C11  110.49  3.000
 GBK  H19  C12  C11  108.62  3.000
 GBK  N15  C12  C11  110.46  3.000
 GBK  H21  N14  C09  109.57  3.000
 GBK  H21  N14  C08  107.77  3.000
 GBK  C09  N14  C08  114.02  3.000
 GBK  H23  N15  C12  109.08  3.000
 GBK  H23  N15  C13  108.85  3.000
 GBK  C12  N15  C13  112.37  3.000
 GBK  H25  C18  C19  119.77  3.000
 GBK  H25  C18  C17  119.55  3.000
 GBK  C19  C18  C17  120.68  3.000
 GBK  H26  C19  C18  119.62  3.000
 GBK  H26  C19  C20  120.06  3.000
 GBK  C18  C19  C20  120.33  3.000
 GBK  C02  O16  C01  118.95  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 GBK  CONST_01  C20  C21  C22  C17     0.00   0.0  0
 GBK  CONST_02  C20  C19  C18  C17     0.00   0.0  0
 GBK  CONST_03  C18  C17  C22  C21     0.00   0.0  0
 GBK  CONST_04  C18  C19  C20  C21     0.00   0.0  0
 GBK  CONST_05  C19  C18  C17  C22     0.00   0.0  0
 GBK  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 GBK  CONST_07  C05  C06  C07  C02     0.00   0.0  0
 GBK  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 GBK  CONST_09  C06  C07  C02  C03     0.00   0.0  0
 GBK  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 GBK  CONST_11  C07  C06  C05  C04     0.00   0.0  0
 GBK  CONST_12  C07  C02  C03  C04     0.00   0.0  0
 GBK  CONST_13  C21  C22  C17  C13   180.00   0.0  0
 GBK  CONST_14  C19  C18  C17  C13   180.00   0.0  0
 GBK  CONST_15  C08  C07  C02  C03   180.00   0.0  0
 GBK  CONST_16  O16  C02  C03  C04   180.00   0.0  0
 GBK  CONST_17  C08  C07  C06  C05   180.00   0.0  0
 GBK  CONST_18  O16  C02  C07  C06   180.00   0.0  0
 GBK  CONST_19  H6   C22  C17  C13     0.00   0.0  0
 GBK  CONST_20  H25  C18  C17  C13     0.00   0.0  0
 GBK  CONST_21  H5   C21  C22  C17   180.00   0.0  0
 GBK  CONST_22  H26  C19  C18  C17   180.00   0.0  0
 GBK  CONST_23  H4   C20  C21  C22   180.00   0.0  0
 GBK  CONST_24  H13  C06  C07  C02   180.00   0.0  0
 GBK  CONST_25  H11  C04  C03  C02   180.00   0.0  0
 GBK  CONST_26  H12  C05  C04  C03   180.00   0.0  0
 GBK  CONST_27  H10  C03  C04  C05   180.00   0.0  0
 GBK  Var_01    N15  C12  C11  C10   -56.10  30.0  1
 GBK  Var_02    C11  C12  N15  C13    59.91  30.0  1
 GBK  Var_03    C12  C11  C10  C09    55.38  30.0  1
 GBK  Var_04    C07  C02  O16  C01   179.19  30.0  2
 GBK  Var_05    N14  C08  C07  C02    73.51  30.0  2
 GBK  Var_06    C09  N14  C08  C07  -177.08  30.0  1
 GBK  Var_07    H7   C01  O16  C02   -62.07  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GBK  chir_01  C13  N15  C09  C17  positiv
 GBK  chir_02  C09  N14  C10  C13  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 GBK  plan-1  C13  0.020
 GBK  plan-1  C17  0.020
 GBK  plan-1  C20  0.020
 GBK  plan-1  C21  0.020
 GBK  plan-1  C22  0.020
 GBK  plan-1  C18  0.020
 GBK  plan-1  C19  0.020
 GBK  plan-1  H4   0.020
 GBK  plan-1  H5   0.020
 GBK  plan-1  H6   0.020
 GBK  plan-1  H25  0.020
 GBK  plan-1  H26  0.020
 GBK  plan-2  C02  0.020
 GBK  plan-2  C03  0.020
 GBK  plan-2  C04  0.020
 GBK  plan-2  C05  0.020
 GBK  plan-2  C06  0.020
 GBK  plan-2  C07  0.020
 GBK  plan-2  C08  0.020
 GBK  plan-2  H10  0.020
 GBK  plan-2  H11  0.020
 GBK  plan-2  H12  0.020
 GBK  plan-2  H13  0.020
 GBK  plan-2  O16  0.020

